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Quantifying orthogonal barcodes for sequence census assays

Booeshaghi, A. Sina and Min, Kyung Hoi (Joseph) and Gehring, Jase and Pachter, Lior (2022) Quantifying orthogonal barcodes for sequence census assays. . (Unpublished)

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Barcode-based sequence census assays utilize custom or random oligonucloetide sequences to label various biological features, such as cell-surface proteins or CRISPR perturbations. These assays all rely on barcode quantification, a task that is complicated by barcode design and technical noise. We introduce a modular approach to quantifying barcodes that achieves speed and memory improvements over existing tools. We also introduce a set of quality control metrics, and accompanying tool, for validating barcode designs.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper Itempachterlab / BMGP_2020 Itempachterlab / kb_python Itempachterlab / qcbc
Booeshaghi, A. Sina0000-0002-6442-4502
Min, Kyung Hoi (Joseph)0000-0003-0894-4017
Gehring, Jase0000-0002-3894-9495
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. The authors have declared no competing interest.
Record Number:CaltechAUTHORS:20230322-101653000.21
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:120314
Deposited By: George Porter
Deposited On:22 Mar 2023 18:07
Last Modified:22 Mar 2023 18:07

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